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annotate tools/cgatools17/tv2vcf.xml @ 5:64017ce705b6 draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools commit c475b4222a15cdadc6085865f4d13426249fec25-dirty
author yhoogstrate
date Wed, 11 Nov 2015 03:51:05 -0500
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1 <tool id="tv2vcf" name="TestVariants-2-VCF" version="v2">
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3 <description> Convert CG MasterVar format to VCF format </description>
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5 <requirements>
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6 <requirement type="package" version="1">cgatools17</requirement>
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7 </requirements>
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9 <command interpreter="perl">
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10 testvariants2VCF-v2.pl $testvarIn ${crr.fields.crr_path} > $output
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11 </command>
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13 <inputs>
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14 <param name="testvarIn" type="data" format="tabular" label="TestVariants file to be converted to VCF"/>
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15 <param name="crr" type="select" label="Reference Build">
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16 <options from_data_table="cg_anno_files" />
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17 </param>
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18 </inputs>
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20 <outputs>
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21 <data format="vcf" name="output" label="${tool.name} on ${on_string}"/>
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22 </outputs>
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23
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24 <help>
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25 This program converts the output of the cgatools *testvariants* command into a multi-sample VCF file.
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27 Variants that share the same location (chr,begin,end) will be merged into one locus and their flags (0,1,N) will be converted into genotype calls.
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28 Samples that are positive for more than two alleles within the same locus will be flagged and their genotype calls set to unknown (./.).
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29 For a non-SNP locus, the VCF format requires that an extra reference base immediately upstream of the variant locus be included in the REF and ALT columns.
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31 Author: Zuoming Deng, zdeng@completegenomics.com
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33 </help>
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34 </tool>